Bioremediation

Environmental biotechnology utilizes microorganisms to improve the environmental quality. These improvements include the treatment of contaminated waters and wastewaters, clean up of industrial waste streams, and remediation of soils contaminated with hazardous and toxic chemicals.
This course will introduce the students to the scientific principles of microbiological treatment technologies to clean up contaminated environments and to the basic DNA engineering techniques to manipulate microorganisms for these purposes. Moreover, the students will acquire experience on molecular methods /techniques used to monitor the presence of contaminants by the construction of a microbial biosensor. The course will consist of lecture-based teaching to provide background information on key concepts on bioremediation and in a laboratory-based section where the students will construct and use a microbial biosensor.
The lecture-based section will include the following topics: (1) fundamentals of environmental microbiology, (2) principles of bioremediation of organic contaminants and toxic molecules, (3) engineering strategies for bioremediation and biosensors construction.

Laboratory section

Day 1: Extraction of genomic DNA from suitable bacterial strain and quantification.
Day 2: Amplification of regulative gene and promoter by PCR, check on agarose gel and excision from agarose gel. Enzymatic digestion of fragment DNA.
Day 3: Plasmid DNA extraction (Midiprep) and purification. Enzymatic digestion.
Day 4: DNA fragment/plasmid excision from agarose gel, set up of the ligation mixture and overnight incubation.
Day 5: Competent Escherichia coli cells preparation and transformation. Overnight incubation.
Day 6 (second week): Plasmid preparation (Miniprep) from transformants and screening by restriction analysis.
Day 7: Growth of the reporter E. coli and control strains in the presence of different xenobiotic compounds and samples collection.
Day 8: β-galactosidase assay. Conclusions.

The effects of toxic agents can be studied on cellular models. Thus the principles of cell biology and cell culture manipulation will be given in this course. Specifically, the students will learn the basic principles of cell cultures including the use of primary and immortalised mammalian cells. Further an overview of the techniques used to study gene and protein expression, as well as gene knockdown and knockout will be given. Further the students will learn how to transfect cells, how to measure proliferation survival, viability, adhesion. migration and invasion. Examples of these methods will be given by presenting articles related to these subjects.
The lecture-based section will include the following topics: (1) fundamentals of cell culture, (2) principles of gene and protein expression, (3) engineering strategies to study the gene function (4) methods to assess protein localisation, cell viability, survival and proliferation; (5) methods to assess cell adhesion, migration and invasion. The practical section will include demonstrations on cell culture, transfection, cell migration and protein localisation.